4d0z: Difference between revisions

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 ==GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)==
-<StructureSection load='4d0z' size='340' side='right' caption='[[4d0z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4d0z' size='340' side='right'caption='[[4d0z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4d0z]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4d0z]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D0Z FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HWU:(2R,3R,4R,5R,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL+[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>HWU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d0t|4d0t]], [[4d11|4d11]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BBK:2-(ACETYLAMINO)-2-DEOXY-5-THIO-ALPHA-D-GALACTOPYRANOSE'>BBK</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HWU:(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl+[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>HWU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polypeptide_N-acetylgalactosaminyltransferase Polypeptide N-acetylgalactosaminyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.41 2.4.1.41] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4d0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0z OCA], [https://pdbe.org/4d0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d0z RCSB], [https://www.ebi.ac.uk/pdbsum/4d0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0z ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0z RCSB], [http://www.ebi.ac.uk/pdbsum/4d0z PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_HUMAN] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4d0z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
+[[Category: Homo sapiens]]
-[[Category: Clausen, H.]]
+[[Category: Large Structures]]
-[[Category: Companon, I.]]
+[[Category: Clausen H]]
-[[Category: Corzana, F.]]
+[[Category: Companon I]]
-[[Category: Hurtado-Guerrero, R.]]
+[[Category: Corzana F]]
-[[Category: Iglesias-Fernandez, J.]]
+[[Category: Hurtado-Guerrero R]]
-[[Category: Kong, Y.]]
+[[Category: Iglesias-Fernandez J]]
-[[Category: Lira-Navarrete, E.]]
+[[Category: Kong Y]]
-[[Category: Peregrina, J M.]]
+[[Category: Lira-Navarrete E]]
-[[Category: Pinto, B M.]]
+[[Category: Peregrina JM]]
-[[Category: Rovira, C.]]
+[[Category: Pinto BM]]
-[[Category: Vocadlo, D.]]
+[[Category: Rovira C]]
-[[Category: Zandberg, W F.]]
+[[Category: Vocadlo D]]
-[[Category: Acetamido group]]
+[[Category: Zandberg WF]]
-[[Category: Bi-bi kinetic mechanism]]
-[[Category: Qm/mm metadynamic]]
-[[Category: Retaining galnac-t2]]
-[[Category: Substrate specificity]]
-[[Category: Substrate-guided sni-type reaction]]
-[[Category: Transferase-peptide complex]]